Rice resources

The "Indirect Dye"method uses
amino allyl dUTP to label the cDNA. This method prevents the dyes
from creating a bias in the cDNA synthesis. The "Direct Dye"
method uses Cy3/Cy5-coupled dUTP for cDNA synthesis. This reduces
the number of steps to make the labeled cDNA. The 3DNA method uses
Genisphere's dendrimer with about 200 dyes per cDNA so the signal
is very strong. You can download the methods we used, and personal
comments from the table below:

Online
Dry-Lab to Explore DeRisi Experiment Teaching resources for working
through the DeRisi diauxic shift paper (1997) using the original data. Ideal
for allowing students to compare their analysis with the published version.
All components are free and can be used with MAGIC
Tool, free microarray software.

GeneSpring
Protocol. Take your data from Scanalyse to GeneSpring. Good for looking
at a series of related experiments (e.g. time course, dose response, etc.)
This protocol was developed by Terrie Rife at James Maddison University.

Online
Dry-Lab to Explore DeRisi Experiment Teaching resources for working
through the DeRisi diauxic shift paper (1997) using the original data. Ideal
for allowing students to compare their analysis with the published version.
All components are free and can be used with MAGIC
Tool, free microarray software.

Turn the slide so that it is a tall rectangle with the slide
number etched at the bottom of the slide, facing up. Then, the Top half has 16 grids
(with the Bottom half being a duplicate). Then, the grids are as follows:

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

Slide Number
(DNA side Up)

Within each grid, the 2nd spot is to the right of the 1st spot,
which is in the top left of each grid.

Basically, once you have the slide oriented, everything is just like a
Book...

You can read a bit about the bar
code method at this web page. We have two pools of mutant cells: heterozygotes and homozygotes.
The homozygotes have both alleles deleted and there are about 4200 strains
pooled into one batch of cells. The heterozygotes have one allele deleted
by the bar code method, and the other allele is wt. These are heterozygotes
because homozygote deletions are lethal; we have about 1800 heterozygote
strains pooled in one batch of cells. We have frozen stocks of these and
can send you what we have as long as they last. We obtained these as a
generous donation from Corey
Nislow who is at the Univeristy of Toronto. The bar code microarrays
are provided directly from Agilent to the end user. GCAT is
billed for these chips and GCAT bills
the end user our normal costs. The list of strains and PCR primers used
to amplify the bar codes from genomic DNA are in the Excel files below.

2007/2008 Fly Chips produced at University
of Oregon have NO LABELS! Please fog them and put a label (etched) on the
same side as the DNA. Then when you send the slides for scanning, be sure
to tell us where the label is relative to DNA. We will have to figure out
the orientation as we go along.

An email said "Jason sent the arrays, so I'm not
sure what he did in the way of etching. Tell them that if they look
at an array and each block looks like this:

..................
..................
..................
.........

"

Campbell suggests:

I strongly suggest you
fog the slides and look at them to try to match this pattern with genelist.
Then you will know where to put your etch mark so we can scan
them in the normal orientation. However, keep in mind that MAGIC
Tool allows you to indicate the correct order for numbering,
so you can recover from any orientation mistakes if you are careful
at the time of addressing
the slide.

Download Gene File for 2006/2007 Fly Chips produced at University
of Oregon
They are long, amino-modified oligo arrays on
aldehyde slides; oligos synthesized by Illumina for
a consortium of fly lab called INDAC.

Chips are from the beginning of the print run, so some spots
might be a little "blobby",
but overall they are very nice arrays.

I etched the back of the array and numbered them. The back does NOT have
the DNA.

Download Gene File for 2005/2006 Fly Chips produced
at University of Oregon
They are long oligo arrays, synthesized by Illumina for a consortium
of fly lab called INDAC.

The DNA is up, the spots are read from left to right. The info in the
GAL file give the predicted fly gene "CG####" for each spot. If
everything is lined up right, the first row of each block should be mostly
control spots that give little signal (Arabidopsis DNA), and have a non-CG####
identifier.

The lab that made these slides uses 25x60mm "lifterslip" coverslips
(available through Erie Scientific, Fisher and
VWR).

They use 40 μL hyb solution per array.

The slides are poly-L-lysine (he thinks).

The oligos are 65- to 70-mers.

The arrays have been post-processed, so steaming and snap-drying shouldn't
be necessary. You can verify this by looking for spots. If you do not see
them, but you can see them when you fog the slide with your breath, then
the chips have been post-(print)-processed.

They're better "fresh" (i.e. used soon) but they are probably
good for "a while".

They should tolerate higher hyb temps (55-65 degrees) but they've only
used formamide buffer and 42 degrees themselves.

Here is the conversion file (HEEBO_Human_Set_v1.00)
for identifying the genes from the oligo names (compare columns F and S).
Also, sequecnes for the oligos are available here. This file is in Excel
format of .xlsx. The
file is very large, so it will take a while.

From Daron Barnard at College of the Holy Cross:Gene
List in Gal Format (3 MB .gal file that opens in Excel if needed)
On the gene list file there
are two columns with identifiers: one is a oligo ID that is not helpful in
searching a database, and then there is the 'Name' column. Some of these
entries have the GI # and the Accession # but they are buried in a FASTA
type format (without the <).
The program that I am using for the analysis of the files is CARMAweb (a
Web based GUI for analysis using R and the BioConductor packages) and after
clustering I can examine any specific gene's expression and link directly
to the gene page for that gene - but the gene list doesn't provide information
in a way that is easily accessible. Also I can do GO-analysis, but again
I need a column that has an identifier that the program recognizes.

In a nut
shell: this extracts the accession number for (many of the) genes (I am
not sure why some do not have accession numbers) in a way that can be easily
read by programs since they are in a separate column.

Download Gene File
for 2002 - 2004/2005Human Chips produced at University
of Miami Medical School

Maize

Store the microarrays
at room temperature protected from light in a dust free environment. Do not
store arrays in the cold room or above 50 °C.

Long-oligo arrays can be
stored up to 12 months at room temperature. Do not forget the re-hydration
and UV crosslinking steps that are needed prior to hybridization.

The DNA
oligos are printed on the labeled side of the slide. When exposing the
slides to either the water vapor for the re-hydration or UV light for crosslinking,
be sure to expose the DNA side of the slide.

At no time before the crosslinking
step are the slides to be immersed in water. Slides may be stored for longer
periods of time after re-hydration and UV crosslinking.

The Genome Sequencing Center at Washington University has received funding
from NHGRI and HHMI to produce and distribute microarrays for use by C.
elegans investigators. We feel that providing a common resource will enable comparability
of microarray data sets between C. elegans laboratories. The microarrays will
contain long oligomers (nominally 60 mer) that are designed to uniquely represent
each gene in C. elegans (one oligo per gene), placed onto treated glass slides
using split pin technology. Also included on-array will be long oligomers representing
unique E. coli genes, thus allowing investigators to assess relative contamination
of input C. elegans RNA samples with E. coli RNA. We also intend to spot up
to 10 different long oligomers that represent unique Arabidopsis thaliana genes.
RNA samples that correspond to each A. thaliana element can be purchased from
Stratagene (www.Stratagene.com) by end-users, and added to their reverse transcription
reactions during work-up of C. elegans samples. This combination of A.
thaliana oligo elements and RNAs will act as controls for cDNA and labeling reactions,
as well as providing a source of array data normalization that is independent
of sample preparation.

Soybeans (starting fall 2007)

Genelists are emailed directly to end users. Not permitted to post them on
this web site.

A standard gal file is provided along with an electronic file providing unique
ID spot locations, 70-mer sequence and the clone ID and Accession number containing
the 70-mer are provided with the slide shipment in Excel format. It is the
responsibility of the users to convert these files to the appropriate format
needed for their own use with their laser scanning equipment.

The oligo arrays have been used in the following publications: Gonzalez and
Vodkin, BMC Genomics 8: 468 (2007).